meshi.symmetryComplex.proteinsGJ
Class GJModeller

java.lang.Object
  meshi.symmetryComplex.proteinsGJ.GJModeller

All Implemented Interfaces:

KeyWords

Direct Known Subclasses:

BackboneCompleterAndMinimizer

public class GJModeller
extends java.lang.Object
implements KeyWords

Created by IntelliJ IDEA. User: TM Date: Dec 23, 2008 Time: 2:36:29 PM To change this template use File | Settings | File Templates.

Nested Class Summary

static class	GJModeller.HBRangesAndGoodResiduesFilter
static class	GJModeller.HBRangesFilter
private static class	GJModeller.SpecialHBPairs

Field Summary

protected SequenceAlignment	alignment
Protein	caHelicesProtein
protected CommandList	commands
protected ResidueCreator	creator
protected static double	DISTANCE_AS_NEIGHBOUR_CHAINS
protected TotalEnergy	energy
SymmetricComplex	gj
static Filter	innerBarrelFilter
protected static int	numberOfChains
static Filter	outerBarrelFilter
protected java.lang.String	outputFileMask
protected Sequence	sequence
protected char	stage
long	startTime Used by Window.
protected static Topology	topology

Fields inherited from interface meshi.util.KeyWords

AA_SEQUENCE, ACCESIBILITY_SEQUENCE, ALINMENT_FILE_PATH, ALL_CA, ALPHA_ANGLE_ENERGY, ALPHA_TORSION_ENERGY, ANGLE_ENERGY, ANGLE_X, ANGLE_Z, ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY, BEAUTIFY_PROBLEMATIC_RANGE, BFGS, BOND_ENERGY, BUFFER_SIZE, CA_CLASH_DISTANCE, CA_LONG_DISTANCE, CA_MODEL, CA_SHORT_DISTANCE, CA_TETHER_ENERGY, CALPHA_HYDROGEN_BONDS, CALPHA_HYDROGEN_BONDS_PLANE, CASP_GROUP, CG, CHECK_INTERLOOP_DISTANCE, CLASH_DISTANCE, COMPOSITE_PROPENSITY_ENERGY, CONSENSUS_ENERGY, CONSTRICT, COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY, COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_FILENAME, COOPERATIVE_PERATOM_SUMMA_ENERGY, COOPERATIVE_PERATOM_SUMMA_FILENAME, COOPERATIVE_PROPENSITY_ENERGY, COOPERATIVE_PROPENSITY_FILENAME, COOPERATIVE_RAMACHANDRAN_ENERGY, COOPERATIVE_RAMACHANDRAN_FILENAME, COOPERATIVE_Z_PROPENSITY_ENERGY, COOPERATIVE_Z_PROPENSITY_FILENAME, COOPERATIVE_Z_RAMACHANDRAN_ENERGY, COOPERATIVE_Z_RAMACHANDRAN_FILENAME, COOPERATIVE_Z_SUMMA_ENERGY, COOPERATIVE_Z_SUMMA_FILENAME, CORPUS_FILE_NAME, CSAonly_FILES_LOCATION_PATH, CUTOFF, CYLINDER_ENERGY, DICTIONARY_KEY, DIELECTRIC_CONSTANT, DISTANCE_CONSTRAINT_PCA, DISTANCE_CONSTRAINTS_ENERGY, DISTANCE_CONSTRAINTS_MASK, DISTANCE_FROM_CENTROID_ENERGY, DRESSER_FRAGMENTS, EDM_ENERGY, EDM_ENERGY_FILE_NAME, ELECTROSTATICS, END, EXCLUDED_VOL, FINAL_TEMPERATURE, FIX_C_TERMINAL, FIX_N_TERMINAL, FLAT_RAMACH_ENERGY, FREE_FINAL_MINIMIZATION, GRID_EDGE, HYDROGEN_BONDS, HYDROGEN_BONDS_ANGLES, HYDROGEN_BONDS_PAIRS, HYDROGEN_BONDS_PLANE, INFLATE_ENERGY, INITIAL_TEMPERATURE, INPUT_FILE, INTER_SEGMENT_FACTOR, INTER_SEGMENT_TOLERANCE, INTRA_SEGMENT_FACTOR, INTRA_SEGMENT_TOLERANCE, ITERATIONS_ALLATOM, ITERATIONS_BACKBONE, ITERATIONS_CA, KEY_KEY, KOEHL_FILE, LBFGS, LENNARD_JONES, LENNARD_JONES_CA, LINEAR_RG, LOOP1, LOOP2, LOOSEN_EDGE_LENGTH, MAX_ANGLE, MAX_CLASHES, MAX_DISTANCE, MAX_RUN_TIME, MAX_STEPS, MAX_WIDTH_OF_HAIRPIN, MCM, MCM_PERTURBATION, MESHILOG_KEY, METHOD, MIN_WIDTH_OF_HAIRPIN, MINIMIZATION_LOOP, MINIMIZE, MODE, MODEL, MODEL_DSSP, MODEL_NUMBER, N_ATOMS, N_TRIES, NON_FROZEN_BOND_DEPTH, NON_FROZEN_RADIUS, NONE, NUMBER, NUMBER_OF_CA_ITERATIONS, NUMBER_OF_CHAINS, NUMBER_OF_MODELS, NUMBER_OF_RUNS, OFF, ON, OPTIMIZER, OUT_OFPLANE_ENERGY, OUTPUT_FILE_NAME, OUTPUT_FILE_PATH, PARAMETERS_DIRECTORY, PDB_FILE, PLANE_ENERGY, PROPENSITY_TORSION_ENERGY, R_MAX, RAMACHANDRAN_SIDECHAIN_ENERGY, REFERENCE, RELAX, REPORT_EVERY, RESTART_EVERY, RMS_TARGET, ROTAMER_LIBRARY, SATURATION, SECONDARY_STRUCTURE, SEED, SEQUENCE, SHOTGUN_MODEL, SMOOTH_ROTAMER_LIBRARY_ENERGY, SOLVATE_ENERGY, SS_NAME, SS_SEQUENCE, STEEPEST_DECENT, STEPS, STRICT_CLASHES, STRUCTURE_NAMES, SUPERIMPOSE, SYMMETRY_ENERGY, TARGET_FILE_PATH, TARGET_NAME, TARGET_SEQUENCE, TEMPLATE_DISTANCE_CONSTRAINTS, TEMPLATE_DSSP, TEMPLATE_ENERGY, TEMPLATE_FILE_PATH, TEMPLATE_NAME, TEMPLATE_STRUCTURE, TEMPLATE_TARGET_ALIGNMENT, TETHER_ENERGY, TOLERANCE, TOPOLOGY_MAP, TWO_TORSIONS_ENERGY, UN_WARP_ENERGY, UNSATISFIED_CUTTOF, UP_TO_CUTOFF, USE_FAST_ARCCOS, VALUE_KEY, VOLUME_CONSTRAINT, WARP_ENERGY, WARP_STEP_SIZE, WARP_THRESHOLD, WEIGHT, WIDTH_OF_HAIRPIN

Constructor Summary

GJModeller(java.lang.String sequence, CommandList commands, java.lang.String outputFileMask)

GJModeller(java.lang.String tmCasPdbLocation, java.lang.String sequence, CommandList commands, java.lang.String outputFileMask)

Method Summary

protected void	backboneRelax()
protected void	caRelax()
ResidueCreator	creator()
private static java.lang.String	fixZero(long num)
void	generateData(java.lang.String stage)
void	generateFiles(SymmetricComplex sc, ResidueCreator creator)
void	generateLoopData(java.lang.String stage)
java.lang.String	getChainLetters(boolean[] chainsBooleans)
protected SymmetricComplex	makeActualSymmetryComplex(SymmetricComplex gjAll, ResidueCreator creator)
protected void	restoreAll(ResidueCreator creator)
protected void	setGJ(java.lang.String tmCasPdbLocation)
void	timeStamp()
protected boolean	toContinue(java.lang.String stage)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

gj

public SymmetricComplex gj

energy

protected TotalEnergy energy

commands

protected CommandList commands

stage

protected char stage

outputFileMask

protected java.lang.String outputFileMask

sequence

protected Sequence sequence

caHelicesProtein

public Protein caHelicesProtein

topology

protected static Topology topology

DISTANCE_AS_NEIGHBOUR_CHAINS

protected static final double DISTANCE_AS_NEIGHBOUR_CHAINS

See Also:

Constant Field Values

numberOfChains

protected static int numberOfChains

alignment

protected SequenceAlignment alignment

creator

protected ResidueCreator creator

startTime

public final long startTime

Used by Window.

innerBarrelFilter

public static Filter innerBarrelFilter

outerBarrelFilter

public static Filter outerBarrelFilter

Constructor Detail

GJModeller

public GJModeller(java.lang.String sequence,
                  CommandList commands,
                  java.lang.String outputFileMask)
           throws java.io.IOException

Throws:

java.io.IOException

GJModeller

public GJModeller(java.lang.String tmCasPdbLocation,
                  java.lang.String sequence,
                  CommandList commands,
                  java.lang.String outputFileMask)
           throws java.io.IOException

Throws:

java.io.IOException

Method Detail

creator

public ResidueCreator creator()

setGJ

protected void setGJ(java.lang.String tmCasPdbLocation)
              throws java.io.IOException

Throws:

java.io.IOException

makeActualSymmetryComplex

protected SymmetricComplex makeActualSymmetryComplex(SymmetricComplex gjAll,
                                                     ResidueCreator creator)
                                              throws java.io.IOException

Throws:

java.io.IOException

restoreAll

protected void restoreAll(ResidueCreator creator)

toContinue

protected boolean toContinue(java.lang.String stage)

caRelax

protected void caRelax()
                throws java.io.IOException

Throws:

java.io.IOException

backboneRelax

protected void backboneRelax()
                      throws java.io.IOException

Throws:

java.io.IOException

generateData

public void generateData(java.lang.String stage)
                  throws java.io.IOException

Throws:

java.io.IOException

generateLoopData

public void generateLoopData(java.lang.String stage)
                      throws java.io.IOException

Throws:

java.io.IOException

timeStamp

public void timeStamp()

fixZero

private static java.lang.String fixZero(long num)

generateFiles

public void generateFiles(SymmetricComplex sc,
                          ResidueCreator creator)
                   throws java.io.IOException

Throws:

java.io.IOException

getChainLetters

public java.lang.String getChainLetters(boolean[] chainsBooleans)